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Hi All,<br>
<br>
the file ending with ".geo" has a complete footprint of all the
geometry restraints used in phenix.refine run. For example, if you want
to check that atom A is bonded to atom B with given bond length, bond
angle, corresponding sigmas, and so on, just find the corresponding
record in ".geo" file. If you don't see it there, then it means this
particular bond (angle, ...) was not restrained.<br>
<br>
Pavel.<br>
<br>
On 10/16/2008 3:16 PM, Engin Ozkan wrote:
<blockquote cite="mid:48F7BD32.70204@stanford.edu" type="cite">
<pre wrap="">I don't have access to phenix, ccp4, or any of my files right now (our
systems are being upgraded), but I'll make some guesses that may help
you, I might be off the mark.
I think the data_link determines the linkage type, so you should have
ALPHA1-4 and BETA1-4 for different mannoses in your parameter file.
You can also call alpha and beta mannoses different names, I think MAN
is usually alpha mannose, and BMA is beta, and give phenix different cif
files to phenix.
I suggest you look into the cif descriptions, runs a few phenix runs,
and convince yourself that everything checks out chemically.
Engin
Patrick Loll wrote:
</pre>
<blockquote type="cite">
<pre wrap="">OK, so I think you are implying that if I feed phenix.refine
the MAN-a-D.cif, it will assume that any MAN residue it encounters in
the PDB file is alpha. Is that right?
Does this mean that if you have examples of both alpha and beta
mannose residues in a structure, you would need to give one of them a
different residue name?
Thanks,
Pat
On 16 Oct 2008, at 4:52 PM, Engin Ozkan wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Patrick,
Let me give my best shot, I don't have my files with me. There might be
some mistakes.
You can give phenix.refine the .cif file on command line for
MAN-a-D.cif, which you can get from ccp4 sketcher (and I think under
phenix, somewhere close to where you found mon_lib_list.cif). Then you
should describe the linkage as an alpha linkage by
data_link = ALPHA1-4 if you have 1-4 linkage, by something like this.
In the mon_lib_list.cif, I believe they have all recognized linkage
types somewhere down the file, where you can see the proper description
for ALPHA1-4, ALPHA1-6, BETA1-4, and other common sugar linkages.
refinement.pdb_interpretation.apply_cif_link {
data_link = ALPHA1-4
residue_selection_1 = chain X and resname MAN and resid 905
residue_selection_2 = chain X and resname MAN and resid 906
}
I also delete hydrogens and the removed O1 in coot before I do
refinement in phenix, but I am not sure if this is necessary (Phenix
supposedly knows the deletion, it is in the description of the bond).
Good luck,
Engin
Patrick Loll wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi all,
I'm starting to use phenix.refine and have some questions about
defining modifications during refinement:
I want to refine a structure that includes several alpha-D-mannose
residues.
I see that mon_lib_list.cif contains, under the "LIST OF
RECOGNIZED MODIFIED MONOMERS," the following line:
MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose
Question:
Where/how do I invoke this modification? I.e., how do I tell the
refinement program that a particular sugar is an alpha, and not a
beta, mannose?
Clearly I can't label the residue MAN-a-D in the PDB file, as this
would step on the chain identifier.
I'm guessing that I label each sugar MAN in the PDB file, and then
insert some instructions about applying the modification in the CIF
file that I supply to the refinement program. However, I'm not able to
find an example of the appropriate syntax.
Thanks,
Pat Loll
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
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<pre wrap="">---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
<a class="moz-txt-link-abbreviated" href="mailto:pat.loll@drexelmed.edu">pat.loll@drexelmed.edu</a> <a class="moz-txt-link-rfc2396E" href="mailto:pat.loll@drexelmed.edu"><mailto:pat.loll@drexelmed.edu></a>
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